When I read chapter 3 it puts Amy's feeling into prospective for me. Amy loves Fiona like a lover rather than a sister. I think Fiona does love Amy but she doesn't realise that she loves Amy not as a sister but rather as a lover. That's why Amy says to Headmistress that they will die as twins. Also Amy says that she "won't be courting Fiona". She thinks that Fiona only loves her as a sister not as a lover that she would have liked. This comes down to the fact that Fiona hasn't realised her feeling fully and that both girls did not communicate to each other what they want.
When they were having a conversation of where they will go and how will they survive, Fiona says that they can pretend to be twin sisters and Amy says that Fiona doesn't look like her sister. It shows that Amy is realist and that the outside world might question why they are together.
Amy did leave but you can't blame someone to be with their mother even if her mother abandoned her. There is a naturally yearning to be with a family member. Amy realises that being with Fiona, there will not be a future that she wants to have with Fiona. Fiona has not realised herself that she loves Amy in a different way. Fiona is angry at Amy for being abandoned a second time in her life and hopefully she gets to heal her wounds and realises that she was in love with Amy so she can move on with her life.
.jpg?1479171692)
